5ZBQ

The Crystal Structure of human neuropeptide Y Y1 receptor with UR-MK299


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of ligand binding modes at the neuropeptide Y Y1receptor

Yang, Z.Han, S.Keller, M.Kaiser, A.Bender, B.J.Bosse, M.Burkert, K.Kogler, L.M.Wifling, D.Bernhardt, G.Plank, N.Littmann, T.Schmidt, P.Yi, C.Li, B.Ye, S.Zhang, R.Xu, B.Larhammar, D.Stevens, R.C.Huster, D.Meiler, J.Zhao, Q.Beck-Sickinger, A.G.Buschauer, A.Wu, B.

(2018) Nature 556: 520-524

  • DOI: 10.1038/s41586-018-0046-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Neuropeptide Y (NPY) receptors belong to the G-protein-coupled receptor superfamily and have important roles in food intake, anxiety and cancer biology <sup>1,2 </sup> . The NPY-Y receptor system has emerged as one of the most complex networks with ...

    Neuropeptide Y (NPY) receptors belong to the G-protein-coupled receptor superfamily and have important roles in food intake, anxiety and cancer biology 1,2 . The NPY-Y receptor system has emerged as one of the most complex networks with three peptide ligands (NPY, peptide YY and pancreatic polypeptide) binding to four receptors in most mammals, namely the Y 1 , Y 2 , Y 4 and Y 5 receptors, with different affinity and selectivity 3 . NPY is the most powerful stimulant of food intake and this effect is primarily mediated by the Y 1 receptor (Y 1 R) 4 . A number of peptides and small-molecule compounds have been characterized as Y 1 R antagonists and have shown clinical potential in the treatment of obesity 4 , tumour 1 and bone loss 5 . However, their clinical usage has been hampered by low potency and selectivity, poor brain penetration ability or lack of oral bioavailability 6 . Here we report crystal structures of the human Y 1 R bound to the two selective antagonists UR-MK299 and BMS-193885 at 2.7 and 3.0 Å resolution, respectively. The structures combined with mutagenesis studies reveal the binding modes of Y 1 R to several structurally diverse antagonists and the determinants of ligand selectivity. The Y 1 R structure and molecular docking of the endogenous agonist NPY, together with nuclear magnetic resonance, photo-crosslinking and functional studies, provide insights into the binding behaviour of the agonist and for the first time, to our knowledge, determine the interaction of its N terminus with the receptor. These insights into Y 1 R can enable structure-based drug discovery that targets NPY receptors.


    Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Regensburg, Germany. max.keller@chemie.uni-regensburg.de.,University of Chinese Academy of Sciences, Beijing, China.,Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Departments of Chemistry and Bioinformatics, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.,Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,Department of Pharmacology, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.,iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Regensburg, Germany.,Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany. abeck-sickinger@uni-leipzig.de.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. beiliwu@simm.ac.cn.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. beiliwu@simm.ac.cn.,University of Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.,National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany.,Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany.,Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuropeptide Y receptor type 1,T4 Lysozyme
A
525Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 3 
Gene Names: NPY1R (NPYR, NPYY1), E
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Neuropeptide Y Y1 receptor with bound UR-MK299
Find proteins for P25929 (Homo sapiens)
Go to Gene View: NPY1R
Go to UniProtKB:  P25929
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9AO
Query on 9AO

Download SDF File 
Download CCD File 
A
N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide
C33 H41 N7 O5
VQHNWOOVOKYJNL-HHHXNRCGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.840α = 90.00
b = 100.680β = 98.76
c = 83.160γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references
  • Version 1.2: 2018-05-09
    Type: Data collection, Database references